LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task

units           real

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 8 10
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data       data.bpti
Reading data file ...
  orthogonal box = (-10 -10 -30) to (50 50 30)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  892 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-10 -10 -30) to (50 50 30)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  906 bonds
  reading angles ...
  1626 angles
  reading dihedrals ...
  2501 dihedrals
  reading impropers ...
  137 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    19 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.014 seconds

special_bonds   charmm
neigh_modify    delay 2 every 1


# ------------- MINIMIZE ----------

minimize 	1e-4 1e-6 1000 10000
Switching to 'neigh_modify every 1 delay 0 check yes' setting during minimization
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 6
For more information see https://docs.lammps.org/err0029 (src/kspace.cpp:330)
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.20327216
  grid = 16 16 16
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031639896
  estimated relative force accuracy = 9.5282607e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 3549 1024
Generated 378 of 378 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.34 | 17.39 | 17.52 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -3075.6497      943.91164     -2131.7381     -380.67775    
       241   0             -4503.3151      749.58684     -3753.7283     -29.038815    
Loop time of 0.388118 on 4 procs for 241 steps with 892 atoms

96.6% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -2131.73809529936  -3753.44165285823   -3753.7282611677
  Force two-norm initial, final = 1086.2055 26.365933
  Force max component initial, final = 310.81136 3.9385293
  Final line search alpha, max atom move = 0.0059668263 0.02350052
  Iterations, force evaluations = 241 463

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.10108    | 0.22639    | 0.31709    |  18.0 | 58.33
Bond    | 0.0066459  | 0.015677   | 0.023149   |   5.1 |  4.04
Kspace  | 0.043344   | 0.13132    | 0.26581    |  24.7 | 33.84
Neigh   | 0.0083774  | 0.0083904  | 0.0084046  |   0.0 |  2.16
Comm    | 0.0028835  | 0.0035147  | 0.0041829  |   0.8 |  0.91
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.002829   |            |       |  0.73

Nlocal:            223 ave         323 max          89 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost:            613 ave         675 max         557 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:          37223 ave       50005 max       20830 min
Histogram: 1 0 0 0 1 0 0 1 0 1

Total # of neighbors = 148892
Ave neighs/atom = 166.91928
Ave special neighs/atom = 10.939462
Neighbor list builds = 15
Dangerous builds = 0
reset_timestep  0

# ------------- RUN ---------------

thermo          100
thermo_style    multi
timestep	8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

velocity        all create 200.0 12345678 dist uniform
#dump            dump1 all atom 100 4pti.dump

fix             1 all nvt temp 200 300 25
fix             cor all filter/corotate m 1.0
  163 = # of size 2 clusters
  0 = # of size 3 clusters
  25 = # of size 4 clusters
  0 = # of size 5 clusters
  100 = # of frozen angles

run             1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Mollified Impulse Method with Corotational Filter: doi:10.1016/j.jcp.2016.12.024

@Article{Fath2017,
 Title ={A Fast Mollified Impulse Method for Biomolecular Atomistic Simulations},
 Author = {L. Fath and M. Hochbruck and C. V. Singh},
 Journal = {Journal of Computational Physics},
 Year = {2017},
 Pages = {180--198},
 Volume = {333},

 Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},
 ISSN = {0021-9991},
 Keywords = {Mollified impulse method},
 Url = {https://www.sciencedirect.com/science/article/pii/S0021999116306787}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.20327216
  grid = 16 16 16
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031639896
  estimated relative force accuracy = 9.5282607e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 3549 1024
Generated 378 of 378 mixed pair_coeff terms from arithmetic mixing rule
Per MPI rank memory allocation (min/avg/max) = 17.52 | 17.82 | 18.14 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =     -3220.3397 KinEng   =       531.1804 Temp     =       200.0000 
PotEng   =     -3751.5200 E_bond   =        42.2799 E_angle  =       345.2600 
E_dihed  =       337.8366 E_impro  =        24.2104 E_vdwl   =      -288.5348 
E_coul   =      -886.3627 E_long   =     -3326.2093 Press    =        83.2346
------------ Step            100 ----- CPU =    0.4318396 (sec) -------------
TotEng   =     -2718.4639 KinEng   =       539.6162 Temp     =       203.1763 
PotEng   =     -3258.0801 E_bond   =       203.2240 E_angle  =       566.1696 
E_dihed  =       397.6787 E_impro  =        34.7678 E_vdwl   =      -248.6454 
E_coul   =      -874.8600 E_long   =     -3336.4148 Press    =       135.8498
------------ Step            200 ----- CPU =    0.8758413 (sec) -------------
TotEng   =     -2665.9243 KinEng   =       622.5865 Temp     =       234.4162 
PotEng   =     -3288.5108 E_bond   =       207.6820 E_angle  =       590.1034 
E_dihed  =       389.1762 E_impro  =        30.5637 E_vdwl   =      -240.8936 
E_coul   =      -926.1787 E_long   =     -3338.9638 Press    =       103.1355
------------ Step            300 ----- CPU =     1.317221 (sec) -------------
TotEng   =     -2669.6519 KinEng   =       617.4397 Temp     =       232.4783 
PotEng   =     -3287.0916 E_bond   =       202.1987 E_angle  =       570.7062 
E_dihed  =       382.4977 E_impro  =        41.1488 E_vdwl   =      -220.7806 
E_coul   =      -921.1056 E_long   =     -3341.7568 Press    =        45.6780
------------ Step            400 ----- CPU =     1.745249 (sec) -------------
TotEng   =     -2618.2150 KinEng   =       650.8570 Temp     =       245.0606 
PotEng   =     -3269.0720 E_bond   =       197.6951 E_angle  =       618.5882 
E_dihed  =       405.6014 E_impro  =        42.3308 E_vdwl   =      -220.7905 
E_coul   =      -967.2914 E_long   =     -3345.2058 Press    =       -96.4000
------------ Step            500 ----- CPU =     2.167838 (sec) -------------
TotEng   =     -2547.1704 KinEng   =       695.9916 Temp     =       262.0547 
PotEng   =     -3243.1619 E_bond   =       243.0234 E_angle  =       599.0284 
E_dihed  =       400.8631 E_impro  =        40.5671 E_vdwl   =      -208.9691 
E_coul   =      -977.7261 E_long   =     -3339.9487 Press    =       102.1584
------------ Step            600 ----- CPU =     2.603588 (sec) -------------
TotEng   =     -2551.8816 KinEng   =       661.5927 Temp     =       249.1028 
PotEng   =     -3213.4743 E_bond   =       224.7832 E_angle  =       638.9772 
E_dihed  =       411.1306 E_impro  =        38.9581 E_vdwl   =      -236.2389 
E_coul   =      -947.2985 E_long   =     -3343.7860 Press    =       -60.1526
------------ Step            700 ----- CPU =     3.035149 (sec) -------------
TotEng   =     -2569.4018 KinEng   =       660.1035 Temp     =       248.5421 
PotEng   =     -3229.5053 E_bond   =       251.5417 E_angle  =       623.3552 
E_dihed  =       404.3791 E_impro  =        39.6184 E_vdwl   =      -222.0019 
E_coul   =      -986.5481 E_long   =     -3339.8496 Press    =       -25.4372
------------ Step            800 ----- CPU =     3.464376 (sec) -------------
TotEng   =     -2454.3924 KinEng   =       759.2014 Temp     =       285.8545 
PotEng   =     -3213.5939 E_bond   =       245.2390 E_angle  =       609.9283 
E_dihed  =       404.8627 E_impro  =        47.8966 E_vdwl   =      -231.2614 
E_coul   =      -951.3731 E_long   =     -3338.8861 Press    =       -72.4358
------------ Step            900 ----- CPU =     3.877616 (sec) -------------
TotEng   =     -2364.1338 KinEng   =       792.6824 Temp     =       298.4608 
PotEng   =     -3156.8163 E_bond   =       254.5701 E_angle  =       687.2421 
E_dihed  =       405.7040 E_impro  =        47.2725 E_vdwl   =      -196.4679 
E_coul   =     -1015.1553 E_long   =     -3339.9818 Press    =         6.2707
------------ Step           1000 ----- CPU =     4.270266 (sec) -------------
TotEng   =     -2311.5630 KinEng   =       819.5503 Temp     =       308.5770 
PotEng   =     -3131.1134 E_bond   =       266.3423 E_angle  =       688.2701 
E_dihed  =       398.8220 E_impro  =        49.3317 E_vdwl   =      -197.7481 
E_coul   =      -993.0023 E_long   =     -3343.1290 Press    =       128.4091
Loop time of 4.27029 on 4 procs for 1000 steps with 892 atoms

Performance: 161.863 ns/day, 0.148 hours/ns, 234.176 timesteps/s, 208.885 katom-step/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2802     | 2.4349     | 3.2901     |  46.6 | 57.02
Bond    | 0.17213    | 0.34633    | 0.47057    |  21.9 |  8.11
Kspace  | 0.09756    | 0.1059     | 0.11568    |   2.3 |  2.48
Neigh   | 0.10647    | 0.10688    | 0.10727    |   0.1 |  2.50
Comm    | 0.18727    | 1.1743     | 2.5162     |  77.8 | 27.50
Output  | 0.00016246 | 0.00018755 | 0.00024898 |   0.0 |  0.00
Modify  | 0.066389   | 0.085823   | 0.10107    |   5.0 |  2.01
Other   |            | 0.01592    |            |       |  0.37

Nlocal:            223 ave         340 max         125 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost:          579.5 ave         628 max         550 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs:          35126 ave       40605 max       25446 min
Histogram: 1 0 0 0 0 0 1 0 1 1

Total # of neighbors = 140504
Ave neighs/atom = 157.5157
Ave special neighs/atom = 10.939462
Neighbor list builds = 192
Dangerous builds = 0

unfix           cor
unfix           1

Total wall time: 0:00:04
